If you are running a multi-boot configuration with Windows and Linux, and using GRUB as the bootloader, you may be headed for trouble. I first ran into this problem about six months or so ago, but I didn't realize what it was until a few weeks ago. I have been running this kind of configuration (Linux and Windows multi-boot) for several years with no problems until this came up.
The first symptom I saw was with installation of Vista SP2, on two of my laptops - the ASUS N10J and HP Pavillion dv2-1010ez. Both came preloaded with Vista SP1. Because I was going to lend at least one of them to someone who wanted to use Vista, last fall I decided to update them both to Vista SP2. Both had the same problem - after thrashing through a LOT of other updates, Windows Update finally offered to download and install SP2. It then spent a very, very long time thrashing around, until it finally said installation was complete and it needed to reboot. When I let it reboot, it went through the "Installing Updates, Please Wait... Phase 1 xx% Done" malarkey, then "Phase 2 xx% Done", each time counting slowly from 1% to 100%. Then it rebooted, and when it came back up it again went into "Installing Updates, Please Wait... Phase 3 xx% Done", and took a very long time to count from 1% until it finally got to 100%. It then sat there thrashing around for another very long time, before it suddenly announced "Update Failed to Install", and it then went back and removed everything it had done with SP2. No more information than that, no hint about what went wrong, what it didn't like, what I should do next, or anything else.
As I said, this happened twice, on two different machines, and on both of them I had done absolutely nothing with Windows beyond booting to make sure they worked. No configuration, no optional software installed or removed, nothing. At the time I wrote it off as just another example of stupid, broken Microsoft software, and told my friends they would have to live with Vista SP1.
I recently received a set of Win7 upgrade disks for the HP Pavillion, and decided to install them before passing that machine on. The compatibility check and preparation procedure from the first disk ran just fine, then it rebooted and told me to insert the Win7 disk. When I did that, it started running "setup copying files"... and then announced that it had run into an unexpected error, and couldn't continue. Grrrr. It's not possible that even Microsoft is this stupid, that a Win7 upgrade on an essentially untouched Windows installation doesn't work. So what could be the problem? I finally realized that the only thing that had changed was the bootloader. So I restored that, ran the Win7 upgrade again, and this time it worked! That reminded me of the previous SP2 problem, so I went to the N10J, restored the Windows bootloader, ran Windows Update, and it installed SP2 successfully this time!
So, a warning. If you are multi-booting Windows and Linux, and using GRUB, don't be surprised if Windows Update starts failing on you. The simple solution is to keep a copy of the MBR, both the Windows and Linux version, which you can put in place as needed.